Allow params to be loaded from stdin as JSON

Signed-off-by: Ben Sherman <[email protected]>

Author: bentsherman

modules/nextflow/src/main/groovy/nextflow/cli/CmdKubeRun.groovy

@@ -88,7 +88,7 @@ class CmdKubeRun extends CmdRun {
     @Override
     void run() {
         final scriptArgs = (args?.size()>1 ? args[1..-1] : []) as List<String>
-        final pipeline = stdin ? '-' : ( args ? args[0] : null )
+        final pipeline = args ? args[0] : null
         if( !pipeline )
             throw new AbortOperationException("No project name was specified")
         if( hasAnsiLogFlag() )

modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy

@@ -156,9 +156,6 @@ class CmdRun extends CmdBase implements HubOptions {
     @Parameter(names=['-latest'], description = 'Pull latest changes before run')
     boolean latest
 
-    @Parameter(names='-stdin', hidden = true)
-    boolean stdin
-
     @Parameter(names = ['-ansi'], hidden = true, arity = 0)
     void setAnsi(boolean value) {
         launcher.options.ansiLog = value
@@ -289,18 +286,10 @@ class CmdRun extends CmdBase implements HubOptions {
     @Override
     String getName() { NAME }
 
-    String getParamsFile() {
-        return paramsFile ?: sysEnv.get('NXF_PARAMS_FILE')
-    }
-
-    boolean hasParams() {
-        return params || getParamsFile()
-    }
-
     @Override
     void run() {
         final scriptArgs = (args?.size()>1 ? args[1..-1] : []) as List<String>
-        final pipeline = stdin ? '-' : ( args ? args[0] : null )
+        final pipeline = args ? args[0] : null
         if( !pipeline )
             throw new AbortOperationException("No project name was specified")
 
@@ -598,20 +587,6 @@ class CmdRun extends CmdBase implements HubOptions {
     protected ScriptFile getScriptFile0(String pipelineName) {
         assert pipelineName
 
-        /*
-         * read from the stdin
-         */
-        if( pipelineName == '-' ) {
-            def file = tryReadFromStdin()
-            if( !file )
-                throw new AbortOperationException("Cannot access `stdin` stream")
-
-            if( revision )
-                throw new AbortOperationException("Revision option cannot be used when running a script from stdin")
-
-            return new ScriptFile(file)
-        }
-
         /*
          * look for a file with the specified pipeline name
          */
@@ -661,171 +636,9 @@ class CmdRun extends CmdBase implements HubOptions {
 
     }
 
-    static protected File tryReadFromStdin() {
-        if( !System.in.available() )
-            return null
-
-        getScriptFromStream(System.in)
-    }
-
-    static protected File getScriptFromStream( InputStream input, String name = 'nextflow' ) {
-        input != null
-        File result = File.createTempFile(name, null)
-        result.deleteOnExit()
-        input.withReader { Reader reader -> result << reader }
-        return result
-    }
-
     @Memoized  // <-- avoid parse multiple times the same file and params
     Map parsedParams(Map configVars) {
-
-        final result = [:]
-
-        // apply params file
-        final file = getParamsFile()
-        if( file ) {
-            def path = validateParamsFile(file)
-            def type = path.extension.toLowerCase() ?: null
-            if( type == 'json' )
-                readJsonFile(path, configVars, result)
-            else if( type == 'yml' || type == 'yaml' )
-                readYamlFile(path, configVars, result)
-        }
-
-        // apply CLI params
-        if( !params )
-            return result
-
-        for( Map.Entry<String,String> entry : params ) {
-            addParam( result, entry.key, entry.value )
-        }
-        return result
-    }
-
-
-    static final private Pattern DOT_ESCAPED = ~/\\\./
-    static final private Pattern DOT_NOT_ESCAPED = ~/(?<!\\)\./
-
-    static protected void addParam(Map params, String key, String value, List path=[], String fullKey=null) {
-        if( !fullKey )
-            fullKey = key
-        final m = DOT_NOT_ESCAPED.matcher(key)
-        if( m.find() ) {
-            final p = m.start()
-            final root = key.substring(0, p)
-            if( !root ) throw new AbortOperationException("Invalid parameter name: $fullKey")
-            path.add(root)
-            def nested = params.get(root)
-            if( nested == null ) {
-                nested = new LinkedHashMap<>()
-                params.put(root, nested)
-            }
-            else if( nested !instanceof Map ) {
-                log.warn "Command line parameter --${path.join('.')} is overwritten by --${fullKey}"
-                nested = new LinkedHashMap<>()
-                params.put(root, nested)
-            }
-            addParam((Map)nested, key.substring(p+1), value, path, fullKey)
-        }
-        else {
-            addParam0(params, key.replaceAll(DOT_ESCAPED,'.'), parseParamValue(value))
-        }
-    }
-
-    static protected void addParam0(Map params, String key, Object value) {
-        if( key.contains('-') )
-            key = kebabToCamelCase(key)
-        params.put(key, value)
-    }
-
-    static protected String kebabToCamelCase(String str) {
-        final result = new StringBuilder()
-        str.split('-').eachWithIndex { String entry, int i ->
-            result << (i>0 ? StringUtils.capitalize(entry) : entry )
-        }
-        return result.toString()
-    }
-
-    static protected parseParamValue(String str) {
-        if ( SysEnv.get('NXF_DISABLE_PARAMS_TYPE_DETECTION') || NF.isSyntaxParserV2() )
-            return str
-
-        if ( str == null ) return null
-
-        if ( str.toLowerCase() == 'true') return Boolean.TRUE
-        if ( str.toLowerCase() == 'false' ) return Boolean.FALSE
-
-        if ( str==~/-?\d+(\.\d+)?/ && str.isInteger() ) return str.toInteger()
-        if ( str==~/-?\d+(\.\d+)?/ && str.isLong() ) return str.toLong()
-        if ( str==~/-?\d+(\.\d+)?/ && str.isDouble() ) return str.toDouble()
-
-        return str
-    }
-
-    private Path validateParamsFile(String file) {
-
-        def result = FileHelper.asPath(file)
-        def ext = result.getExtension()
-        if( !VALID_PARAMS_FILE.contains(ext) )
-            throw new AbortOperationException("Not a valid params file extension: $file -- It must be one of the following: ${VALID_PARAMS_FILE.join(',')}")
-
-        return result
-    }
-
-    static private Pattern PARAMS_VAR = ~/(?m)\$\{(\p{javaJavaIdentifierStart}\p{javaJavaIdentifierPart}*)}/
-
-    protected String replaceVars0(String content, Map binding) {
-        content.replaceAll(PARAMS_VAR) { List<String> matcher ->
-            // - the regex matcher is represented as list
-            // - the first element is the matching string ie. `${something}`
-            // - the second element is the group content ie. `something`
-            // - make sure the regex contains at least a group otherwise the closure
-            // parameter is a string instead of a list of the call fail
-            final placeholder = matcher.get(0)
-            final key = matcher.get(1)
-
-            if( !binding.containsKey(key) ) {
-                final msg = "Missing params file variable: $placeholder"
-                if(NF.strictMode)
-                    throw new AbortOperationException(msg)
-                log.warn msg
-                return placeholder
-            }
-
-            return binding.get(key)
-        }
-    }
-
-    private void readJsonFile(Path file, Map configVars, Map result) {
-        try {
-            def text = configVars ? replaceVars0(file.text, configVars) : file.text
-            def json = (Map<String,Object>) new JsonSlurper().parseText(text)
-            json.forEach((name, value) -> {
-                addParam0(result, name, value)
-            })
-        }
-        catch (NoSuchFileException | FileNotFoundException e) {
-            throw new AbortOperationException("Specified params file does not exist: ${file.toUriString()}")
-        }
-        catch( Exception e ) {
-            throw new AbortOperationException("Cannot parse params file: ${file.toUriString()} - Cause: ${e.message}", e)
-        }
-    }
-
-    private void readYamlFile(Path file, Map configVars, Map result) {
-        try {
-            def text = configVars ? replaceVars0(file.text, configVars) : file.text
-            def yaml = (Map<String,Object>) new Yaml().load(text)
-            yaml.forEach((name, value) -> {
-                addParam0(result, name, value)
-            })
-        }
-        catch (NoSuchFileException | FileNotFoundException e) {
-            throw new AbortOperationException("Specified params file does not exist: ${file.toUriString()}")
-        }
-        catch( Exception e ) {
-            throw new AbortOperationException("Cannot parse params file: ${file.toUriString()}", e)
-        }
+        return new ParamsCollector(params, paramsFile).apply(configVars)
     }
 
 }